rs3019279

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012415.3(RAD54B):​c.304+22591C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,766 control chromosomes in the GnomAD database, including 12,730 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.41 ( 12730 hom., cov: 32)

Consequence

RAD54B
NM_012415.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.246
Variant links:
Genes affected
FSBP (HGNC:43653): (fibrinogen silencer binding protein) Enables identical protein binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
RAD54B (HGNC:17228): (RAD54 homolog B) The protein encoded by this gene belongs to the DEAD-like helicase superfamily. It shares similarity with Saccharomyces cerevisiae RAD54 and RDH54, both of which are involved in homologous recombination and repair of DNA. This protein binds to double-stranded DNA, and displays ATPase activity in the presence of DNA. This gene is highly expressed in testis and spleen, which suggests active roles in meiotic and mitotic recombination. Homozygous mutations of this gene were observed in primary lymphoma and colon cancer. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FSBPNM_001256141.2 linkuse as main transcriptc.374+818C>G intron_variant ENST00000481490.3
RAD54BNM_012415.3 linkuse as main transcriptc.304+22591C>G intron_variant ENST00000336148.10
RAD54BNM_001205262.3 linkuse as main transcriptc.305-3021C>G intron_variant
RAD54BNM_001205263.2 linkuse as main transcriptc.-249+818C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RAD54BENST00000336148.10 linkuse as main transcriptc.304+22591C>G intron_variant 1 NM_012415.3 P1Q9Y620-1
FSBPENST00000481490.3 linkuse as main transcriptc.374+818C>G intron_variant 1 NM_001256141.2 P1O95073-1

Frequencies

GnomAD3 genomes
AF:
0.407
AC:
61780
AN:
151648
Hom.:
12725
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.407
Gnomad AMI
AF:
0.313
Gnomad AMR
AF:
0.505
Gnomad ASJ
AF:
0.376
Gnomad EAS
AF:
0.466
Gnomad SAS
AF:
0.426
Gnomad FIN
AF:
0.434
Gnomad MID
AF:
0.436
Gnomad NFE
AF:
0.378
Gnomad OTH
AF:
0.429
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.407
AC:
61821
AN:
151766
Hom.:
12730
Cov.:
32
AF XY:
0.414
AC XY:
30683
AN XY:
74150
show subpopulations
Gnomad4 AFR
AF:
0.407
Gnomad4 AMR
AF:
0.505
Gnomad4 ASJ
AF:
0.376
Gnomad4 EAS
AF:
0.465
Gnomad4 SAS
AF:
0.425
Gnomad4 FIN
AF:
0.434
Gnomad4 NFE
AF:
0.378
Gnomad4 OTH
AF:
0.425
Alfa
AF:
0.403
Hom.:
1723
Bravo
AF:
0.414
Asia WGS
AF:
0.426
AC:
1478
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
11
DANN
Benign
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3019279; hg19: chr8-95447905; API